LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Simple rigid body system

units           lj
atom_style      atomic

pair_style      lj/cut 2.5

read_data       data.rigid
Reading data file ...
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  81 atoms
  read_data CPU = 0.000 seconds

velocity        all create 100.0 4928459

# 2 chains of connected bodies

group           clump1 id <> 1 9
9 atoms in group clump1
group           clump2 id <> 9 18
10 atoms in group clump2
group           clump3 id <> 18 27
10 atoms in group clump3
group           clump4 id <> 27 36
10 atoms in group clump4
group           clump5 id <> 37 45
9 atoms in group clump5
group           clump6 id <> 45 54
10 atoms in group clump6
group           clump7 id <> 54 63
10 atoms in group clump7
group           clump8 id <> 63 72
10 atoms in group clump8
group           clump9 id <> 72 81
10 atoms in group clump9

#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
fix 1 all poems group clump1 clump2 clump3 clump4      clump5 clump6 clump7 clump8 clump9
2 clusters, 9 bodies, 7 joints, 81 atoms

neigh_modify    exclude group clump1 clump1
neigh_modify    exclude group clump2 clump2
neigh_modify    exclude group clump3 clump3
neigh_modify    exclude group clump4 clump4
neigh_modify    exclude group clump5 clump5
neigh_modify    exclude group clump6 clump6
neigh_modify    exclude group clump7 clump7
neigh_modify    exclude group clump8 clump8
neigh_modify    exclude group clump9 clump9

thermo          100

#dump           1 all atom 50 dump.rigid.poems2

#dump           2 all image 100 image.*.jpg type type #               axes yes 0.8 0.02 view 60 -30
#dump_modify    2 pad 5

#dump           3 all movie 100 movie.mpg type type #               axes yes 0.8 0.02 view 60 -30
#dump_modify    3 pad 5

timestep        0.0001
thermo          50
run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix poems command:

@Article{Mukherjee08,
 author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
 title = {Substructured molecular dynamics using multibody dynamics algorithms},
 journal = {Intl.~J.~Non-linear Mechanics},
 year =    2008,
 volume =  43,
 pages =   {1045--1055}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 18 18 18
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.666 | 3.666 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    196.00047    3632.2347            0    3668.5311   -2.7403788 
      50    12774.759    1538.7382            0    3904.4344    18.086359 
     100    19803.641    237.21132            0    3904.5523   -3.1528278 
     150      20259.6    152.62072            0    3904.3985   -4.6173524 
     200    20705.978    69.977442            0    3904.4178    9.0928158 
     250    19552.211    283.50525            0     3904.285    15.670465 
     300    19266.324     333.5792            0    3901.4169    7.2119197 
     350    20738.325    63.738945            0    3904.1694    -23.03999 
     400    20616.682    86.082444            0    3903.9864   -13.783584 
     450    19831.326    230.13858            0    3902.6063   0.42074361 
     500    20365.825    131.47231            0    3902.9213    0.6921524 
     550    20794.102    52.163238            0    3902.9229    4.5895354 
     600    20853.873    40.899172            0    3902.7275    2.3593042 
     650    19255.802    336.29509            0    3902.1844    10.341742 
     700    18526.969    471.02462            0    3901.9448  -0.61898691 
     750    18960.662    391.26068            0    3902.4944     12.04731 
     800    20142.432    172.05177            0    3902.1317    4.6838621 
     850     19932.48    210.71175            0    3901.9118    3.4716043 
     900    20243.528    153.13972            0    3901.9411    3.6490762 
     950    20388.132    126.88722            0    3902.4671   -4.4518463 
    1000    20076.333    184.61915            0    3902.4586    -2.272315 
    1050    20859.506    39.696993            0    3902.5684      6.45166 
    1100    15284.661    1072.1908            0    3902.6836    21.194042 
    1150    19658.317    261.99809            0    3902.4272    -2.874422 
    1200    20767.681    56.717094            0    3902.5839   -34.817444 
    1250    20625.583    82.586399            0    3902.1388    11.697329 
    1300    20690.013    71.006478            0    3902.4903   -29.292777 
    1350    20936.019    26.022786            0    3903.0634    1.0316025 
    1400    19753.559    244.81785            0    3902.8844    6.7138514 
    1450    15690.149      998.342            0    3903.9252    48.124557 
    1500    20234.455    155.92516            0    3903.0465     13.17221 
    1550    20779.631    55.063009            0    3903.1428    -2.639045 
    1600    20642.753    80.233905            0    3902.9659   -2.4688467 
    1650    18785.696    423.90402            0    3902.7365   -5.6466663 
    1700    20965.076    20.760444            0     3903.182  -0.45364296 
    1750    18935.406    396.96067            0    3903.5173    25.913302 
    1800    20581.559    91.756972            0    3903.1567    3.8217234 
    1850    20616.946    85.184849            0    3903.1378    4.1907972 
    1900    16602.053    828.40949            0    3902.8637  -0.49505122 
    1950    20175.526    166.53362            0    3902.7421     5.603825 
    2000    20261.924    150.39322            0    3902.6014    -1.196958 
    2050    20170.339    167.40504            0    3902.6531  -0.80849882 
    2100    19820.132    231.26755            0    3901.6624    3.1476607 
    2150     20666.19    75.838461            0    3902.9106   0.53899287 
    2200     19873.51    222.53286            0    3902.8124    7.9310276 
    2250    18548.063    467.69698            0    3902.5235    16.905356 
    2300     20616.61    84.762399            0    3902.6531   -6.7872951 
    2350    18167.738    538.13635            0    3902.5322   -11.458285 
    2400    20120.227    177.01954            0    3902.9875   -1.2593018 
    2450    20436.599    118.32469            0    3902.8801   -6.5989174 
    2500    18919.923    400.26361            0    3903.9531     32.37476 
    2550    19675.809    259.77151            0    3903.4398    19.437327 
    2600    19739.842    247.86388            0    3903.3901    -7.519784 
    2650    20557.026    96.530313            0     3903.387   0.60211646 
    2700    20666.602    76.099892            0    3903.2484   0.16825503 
    2750    20924.585    28.453883            0    3903.3771    2.4227171 
    2800    20360.659     132.8596            0     3903.352    4.1440877 
    2850    20783.475    54.518625            0    3903.3102  -0.57312067 
    2900    20456.181    115.03745            0    3903.2191   -20.118887 
    2950    20779.493    55.321394            0    3903.3756  -0.26783079 
    3000    20011.867    197.30216            0    3903.2035   -1.4704201 
    3050    20741.875    62.208723            0    3903.2966   -7.5432815 
    3100    21001.754    14.148298            0     3903.362    2.9676438 
    3150    20244.086    154.44639            0    3903.3512   -1.9071213 
    3200    20639.615    81.136426            0    3903.2873    1.4826467 
    3250    20735.244    63.529571            0    3903.3895    2.1127055 
    3300    20142.891    173.22282            0    3903.3878    4.7739415 
    3350    19963.765    206.21899            0    3903.2126    5.5410771 
    3400    16628.667    824.13627            0     3903.519    36.087673 
    3450    19228.218    342.81569            0    3903.5968    3.1057274 
    3500    19759.293    244.57876            0     3903.707    2.2339557 
    3550     19853.21    227.06362            0     3903.584   -1.0882119 
    3600    19673.516    260.64854            0    3903.8923    -10.63775 
    3650    19619.238     270.5393            0    3903.7316   -6.3746003 
    3700    20756.865    59.790243            0    3903.6542   -8.3015766 
    3750    20265.025    150.47347            0    3903.2559   -5.7284695 
    3800    20944.683    24.669276            0    3903.3142 -0.070552298 
    3850    19344.831    320.59492            0     3902.971    13.040749 
    3900    19978.209    203.00247            0    3902.6708   0.15638133 
    3950    19864.118    224.19359            0     3902.734     0.453229 
    4000    17606.216    642.71493            0    3903.1252   -12.656002 
    4050    18017.895    566.54102            0    3903.1883    12.133906 
    4100    20092.963    182.17593            0     3903.095    7.7445947 
    4150    20555.337    96.395074            0     3902.939   -6.5429752 
    4200    20709.781    67.869199            0    3903.0138   -2.8653003 
    4250    18956.203    392.20748            0    3902.6155   -1.6249728 
    4300    17816.204    603.72704            0    3903.0241    23.089239 
    4350    18979.742    388.04678            0    3902.8138    3.2511108 
    4400    20272.085    148.82367            0    3902.9135    1.9518268 
    4450    18820.003    417.74789            0    3902.9337    6.3979299 
    4500    19991.936    200.50131            0    3902.7117    3.5118553 
    4550    20915.092    29.663898            0    3902.8291   -2.3174641 
    4600     20690.37    71.125087            0    3902.6752   -12.008575 
    4650     18893.76    404.50849            0    3903.3529    15.006184 
    4700    18611.123     456.1263            0    3902.6306   -5.3574892 
    4750    20497.821     106.5856            0    3902.4784   0.85039837 
    4800    20803.214    50.120522            0    3902.5675    3.8610873 
    4850    18849.598    411.72635            0    3902.3927    9.2029058 
    4900    18121.714    546.68042            0    3902.5533    9.4522272 
    4950    20377.499    128.99323            0    3902.6041    5.3825395 
    5000    20686.114    72.039749            0    3902.8016    -5.706271 
    5050    20180.449    165.51368            0     3902.634   -16.418461 
    5100    20274.947    148.36657            0    3902.9864   -5.6668309 
    5150    18042.324    560.74137            0    3901.9125    3.6791541 
    5200    20794.666    52.204446            0    3903.0685   -1.4517721 
    5250     19073.55    371.18834            0    3903.3272   -13.457439 
    5300    20821.412    47.364313            0    3903.1813     2.258098 
    5350    20583.073    91.271191            0    3902.9513    5.4323985 
    5400    20490.967    108.41184            0    3903.0353     4.122905 
    5450     18141.79    543.66874            0    3903.2594  -0.19951075 
    5500    20274.012    148.55528            0     3903.002    5.0489974 
    5550    17806.237    605.43454            0    3902.8858     43.80619 
    5600    20999.825    14.341937            0    3903.1983    1.0879933 
    5650    20930.929    27.025347            0    3903.1234   -7.0860209 
    5700    20677.725    73.853093            0    3903.0614    2.6864775 
    5750    20521.264    102.87509            0    3903.1092    2.6940548 
    5800    20792.571    52.596021            0    3903.0721    1.2910217 
    5850    20518.674    103.26595            0    3903.0204   -9.2547271 
    5900    18417.885    491.66696            0    3902.3865   -12.049357 
    5950    17243.837    709.37858            0    3902.6817   -6.2357188 
    6000    20262.525    149.56918            0    3901.8885  -0.28964823 
    6050    19883.554    219.14043            0    3901.2801    2.3071707 
    6100    16548.178    838.47869            0     3902.956   -11.715644 
    6150    19601.177    272.14674            0    3901.9944   -0.9008056 
    6200    20499.796     106.2363            0    3902.4949   0.79071424 
    6250    19601.106    272.50139            0    3902.3359   -1.9306693 
    6300    17210.685    712.70535            0    3899.8692    4.8890923 
    6350    19911.896    214.91041            0    3902.2985    12.691129 
    6400    18834.642    411.87123            0    3899.7678   -1.9447856 
    6450    20216.311    158.39781            0    3902.1591    2.6009109 
    6500    20452.025    114.97122            0    3902.3832   0.14644416 
    6550    19142.589    357.34097            0    3902.2649    2.8968485 
    6600    20412.915    122.08784            0    3902.2573    3.1343105 
    6650    17317.867    699.39994            0    3906.4123     42.25563 
    6700    20479.771     109.8036            0    3902.3537    1.3520625 
    6750    20306.902    142.12484            0    3902.6623    2.2032106 
    6800    20755.367    58.994834            0    3902.5814  -0.90518094 
    6850    20471.259     111.7197            0    3902.6936    1.5799331 
    6900    20702.025     69.15032            0    3902.8586    9.3910371 
    6950    20477.695    110.34414            0    3902.5099    1.8181164 
    7000    20560.727    95.057704            0    3902.5998   -15.686006 
    7050    20336.675    136.39386            0    3902.4448    1.3704327 
    7100    20757.399    58.950153            0     3902.913   -6.4250981 
    7150    20870.958    38.095649            0     3903.088   -4.1962169 
    7200    20706.869    68.489134            0    3903.0944    2.8322659 
    7250    20386.713     127.7432            0    3903.0604    6.0287391 
    7300    18391.773    497.21001            0    3903.0939    19.202343 
    7350    20178.898     166.4993            0    3903.3322    1.5682417 
    7400    16858.704    781.78682            0    3903.7691    21.317514 
    7450    17509.513    660.71963            0    3903.2221   -5.9456143 
    7500    19974.601    204.20412            0    3903.2043  -0.69202711 
    7550    20917.053     29.73415            0    3903.2626   -3.9962577 
    7600    20923.518    28.482703            0    3903.2083   -1.9016251 
    7650    20549.528    97.630612            0    3903.0987    3.5512257 
    7700    20861.441    39.903885            0    3903.1337    2.4426264 
    7750    18843.349    413.64461            0    3903.1537     2.677739 
    7800    20616.054    85.214364            0    3903.0021    3.9639004 
    7850    16478.851    851.93376            0    3903.5728    7.3763128 
    7900    20312.115    141.35103            0    3902.8539    4.6707271 
    7950    20389.623    127.16589            0    3903.0219    3.4414001 
    8000    20452.117    115.30715            0    3902.7362   -1.0162528 
    8050    20857.093    40.791886            0    3903.2164   -15.150068 
    8100    19817.543     233.4997            0     3903.415   0.89346046 
    8150    18649.521     449.9112            0    3903.5262  -0.40053588 
    8200    19619.276    270.37616            0    3903.5754    5.5161492 
    8250    20393.176    127.01336            0    3903.5275     2.122613 
    8300    19145.912    358.00424            0    3903.5435     3.863924 
    8350    19636.311    267.17226            0    3903.5262   -7.1496084 
    8400    19086.332    368.86693            0    3903.3729    7.0968952 
    8450    19494.416    292.89527            0    3902.9723    3.1750935 
    8500    20041.919    191.77756            0     3903.244   0.95215503 
    8550    20357.561    133.15478            0    3903.0736  -0.14020152 
    8600    16998.797    756.07003            0    3903.9954   -16.724408 
    8650     20853.26    41.386996            0    3903.1017   -3.2612965 
    8700    20767.768    57.360884            0    3903.2438    1.1157649 
    8750    20752.546    60.106518            0    3903.1705   0.39130547 
    8800    20574.407     92.99798            0    3903.0734   0.61728166 
    8850     20326.99    138.94203            0    3903.1995   -1.9434522 
    8900    17408.108    679.53222            0    3903.2559    21.935371 
    8950     20471.21     112.2721            0    3903.2368    1.8142747 
    9000    19129.591    360.35257            0    3902.8694    4.5786395 
    9050    20439.668    117.89541            0    3903.0191    2.5585685 
    9100    20780.375    54.788664            0    3903.0062    3.8312459 
    9150    19904.559    216.61504            0    3902.6445    12.150414 
    9200    20961.295     21.52065            0    3903.2419   -0.2120699 
    9250    19315.252    326.44175            0    3903.3402   -19.740867 
    9300    20653.002     78.77764            0    3903.4076   -7.8068233 
    9350    18961.572    391.20947            0    3902.6117   -12.660843 
    9400    16262.179    892.67633            0     3904.191      22.2435 
    9450    17064.394    743.33301            0     3903.406    36.139436 
    9500    18075.588    555.06436            0    3902.3954    24.598176 
    9550    20487.738    109.06287            0    3903.0884    2.6320759 
    9600    20358.609    133.36993            0    3903.4828   0.76449113 
    9650    19849.022    228.46312            0     3904.208    9.5547064 
    9700    20448.112     116.8757            0    3903.5632   -1.0845697 
    9750     20472.78    112.51661            0    3903.7722  -0.30676738 
    9800     19491.99    293.35361            0    3902.9814    -20.10857 
    9850    19895.603    218.42479            0    3902.7957  -0.18235641 
    9900    19704.336    254.55068            0    3903.5019    14.553184 
    9950    17689.462     627.9788            0     3903.805    4.9918088 
   10000    20184.205    165.29396            0    3903.1097    2.9472364 
Loop time of 2.2898 on 1 procs for 10000 steps with 81 atoms

Performance: 37732.583 tau/day, 4367.197 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.053341   | 0.053341   | 0.053341   |   0.0 |  2.33
Neigh   | 0.056174   | 0.056174   | 0.056174   |   0.0 |  2.45
Comm    | 0.0087028  | 0.0087028  | 0.0087028  |   0.0 |  0.38
Output  | 0.0036774  | 0.0036774  | 0.0036774  |   0.0 |  0.16
Modify  | 2.1598     | 2.1598     | 2.1598     |   0.0 | 94.32
Other   |            | 0.008128   |            |       |  0.35

Nlocal:             81 ave          81 max          81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:            113 ave         113 max         113 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            582 ave         582 max         582 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 582
Ave neighs/atom = 7.1851852
Neighbor list builds = 993
Dangerous builds = 950
Total wall time: 0:00:02
